VMD-L Mailing List

From: Tim Lo (timlo_at_hku.hk)
Date: Fri Jan 31 2014 - 20:11:55 CST

I have a question about the parametrization of molecules involving a C-C
triple bond. Take 1,2-diphenylethyne (ph-C-triple-C-ph) as an example.
When I use FFTK to parametrize it, the Gaussian job of Hessian
calculation (hess.gau) cannot be performed properly. From the error
message in the Gaussian output file, I think, at least for the default
hess.gau, Gaussian cannot deal with molecules involving a linear moiety.
If so, how can I parametrize a molecule involving a C-C triple bond,
esp. the angle energy terms?

The CGenFF parameter file has 2-butyne as an example of C-C triple bond.
There are indeed some angle energy terms including the sp-C (CG1T1)
atom. Actually, how does one get these terms? There must be some ways to
parametrize this kind of molecules but I cannot figure it out. Can
anyone help? Thank you.

Regards,
Tim